hiPSC models of Schizophrenia
Public release of data and code from Hoffman, et al. (submitted)
Developed by Gabriel Hoffman
Run on 2017-06-21
Data is available on Synapse.
Summary
Plot expression around CNV regions
Report p-value testing if genes in the CNV region in donor with that CNV has gene expression pattern that is sidnificantly different from other donors. Only report if there are > 5 genes in the region
## 581 :
## P-value: 0.9148547
## 676 :
## P-value: 0.1808107
## 676 :
## P-value: 0.0007155458
## 1275 :
## P-value: 3.425329e-39
## 1358 :
## 1358 :
## 1442 :
## P-value: 0.01972795
## 1804 :
## 2011 :
## P-value: 3.813874e-18plot CNV’s
SessionInfo
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.5 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices datasets utils
## [8] methods base
##
## other attached packages:
## [1] WGCNA_1.51 fastcluster_1.1.22
## [3] dynamicTreeCut_1.63-1 pheatmap_1.0.8
## [5] GSEABase_1.36.0 graph_1.52.0
## [7] annotate_1.52.1 XML_3.98-1.5
## [9] HTSanalyzeR_2.26.0 igraph_1.0.1
## [11] gage_2.24.0 GGally_1.3.0
## [13] qvalue_2.6.0 lmerTest_2.0-33
## [15] lme4_1.1-12 Matrix_1.2-8
## [17] variancePartition_1.5.9 ggbio_1.22.3
## [19] EnsDb.Hsapiens.v70_0.0 ensembldb_1.6.2
## [21] GenomicFeatures_1.26.2 AnnotationDbi_1.36.2
## [23] ggrepel_0.6.5 ggplot2_2.2.1
## [25] reshape2_1.4.2 knitr_1.15.1
## [27] xtable_1.8-2 colortools_0.1.5
## [29] preprocessCore_1.36.0 DESeq2_1.14.1
## [31] SummarizedExperiment_1.4.0 Biobase_2.34.0
## [33] GenomicRanges_1.26.2 GenomeInfoDb_1.10.3
## [35] IRanges_2.8.1 S4Vectors_0.12.1
## [37] BiocGenerics_0.20.0 readr_1.0.0
## [39] latex2exp_0.4.0 mixtools_1.0.4
## [41] ape_4.1 gridExtra_2.2.1
## [43] edgeR_3.16.5 limma_3.28.21
## [45] synapseClient_1.14-2 doParallel_1.0.10
## [47] iterators_1.0.8 foreach_1.4.3
##
## loaded via a namespace (and not attached):
## [1] backports_1.0.5 Hmisc_4.0-2
## [3] AnnotationHub_2.6.4 plyr_1.8.4
## [5] lazyeval_0.2.0 splines_3.3.2
## [7] gmp_0.5-13 BiocParallel_1.8.1
## [9] digest_0.6.12 BiocInstaller_1.24.0
## [11] htmltools_0.3.5 GO.db_3.4.0
## [13] gdata_2.17.0 magrittr_1.5
## [15] checkmate_1.8.2 memoise_1.0.0
## [17] BSgenome_1.42.0 cluster_2.0.5
## [19] prada_1.50.0 Biostrings_2.42.1
## [21] matrixStats_0.51.0 colorspace_1.3-2
## [23] rrcov_1.4-3 RCurl_1.95-4.8
## [25] genefilter_1.56.0 impute_1.48.0
## [27] survival_2.40-1 VariantAnnotation_1.20.2
## [29] gtable_0.2.0 zlibbioc_1.20.0
## [31] XVector_0.14.0 RankProd_3.0.0
## [33] Rmpfr_0.6-1 cellHTS2_2.38.0
## [35] DEoptimR_1.0-8 scales_0.4.1
## [37] mvtnorm_1.0-5 vsn_3.42.3
## [39] DBI_0.5-1 Rcpp_0.12.10
## [41] htmlTable_1.9 foreign_0.8-67
## [43] OrganismDbi_1.16.0 Formula_1.2-1
## [45] htmlwidgets_0.8 httr_1.2.1
## [47] gplots_3.0.1 RColorBrewer_1.1-2
## [49] acepack_1.4.1 reshape_0.8.6
## [51] nnet_7.3-12 locfit_1.5-9.1
## [53] labeling_0.3 munsell_0.4.3
## [55] tools_3.3.2 RSQLite_1.1-2
## [57] evaluate_0.10 stringr_1.2.0
## [59] yaml_2.1.14 robustbase_0.92-7
## [61] caTools_1.17.1 KEGGREST_1.14.0
## [63] RBGL_1.50.0 nlme_3.1-131
## [65] mime_0.5 BioNet_1.34.0
## [67] biomaRt_2.30.0 compiler_3.3.2
## [69] pbkrtest_0.4-6 png_0.1-7
## [71] interactiveDisplayBase_1.12.0 affyio_1.44.0
## [73] tibble_1.2 geneplotter_1.52.0
## [75] pcaPP_1.9-61 stringi_1.1.2
## [77] lattice_0.20-34 nloptr_1.0.4
## [79] data.table_1.10.4 bitops_1.0-6
## [81] httpuv_1.3.3 rtracklayer_1.34.2
## [83] colorRamps_2.3 R6_2.2.0
## [85] latticeExtra_0.6-28 affy_1.52.0
## [87] KernSmooth_2.23-15 codetools_0.2-15
## [89] dichromat_2.0-0 boot_1.3-18
## [91] MASS_7.3-45 gtools_3.5.0
## [93] assertthat_0.1 Category_2.40.0
## [95] rprojroot_1.2 rjson_0.2.15
## [97] GenomicAlignments_1.10.0 Rsamtools_1.26.1
## [99] grid_3.3.2 rpart_4.1-10
## [101] minqa_1.2.4 rmarkdown_1.3
## [103] segmented_0.5-1.4 biovizBase_1.22.0
## [105] shiny_1.0.0 base64enc_0.1-3